Missed-base appeal -- does first run count?

[bw22]

OK, runners on second and third. Two outs. Double to left center.
Runner from second misses third. By a lot. Called out on appeal after play ends.

Our umpire said the first run -- the runner who was on third and scored long before the appeal -- did not count.

I say it does -- the appeal out should not be treated like a force-out, which clearly would make the first run not score.

Help, please!!!!! Even our league president didn't know the rule.